rs17723470

Positions:

• chr11-45206016-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001384648.1(PRDM11):​c.554+1238C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,172 control chromosomes in the GnomAD database, including 3,998 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3998 hom., cov: 33)
• Consequence: PRDM11 NM_001384648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

PRDM11 (HGNC:13996): (PR/SET domain 11) Predicted to enable chromatin binding activity. Involved in several processes, including negative regulation of cell growth; positive regulation of fibroblast apoptotic process; and regulation of transcription, DNA-templated. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDM11	NM_001384648.1	c.554+1238C>T		intron_variant		ENST00000683152.1	NP_001371577.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDM11	ENST00000683152.1	c.554+1238C>T		intron_variant			NM_001384648.1	ENSP00000507575	P1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32299 AN: 152054 Hom.: 3998 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.198

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.212 AC: 32311 AN: 152172 Hom.: 3998 Cov.: 33 AF XY: 0.212 AC XY: 15780 AN XY: 74382

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0472

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.196

Alfa AF: 0.251 Hom.: 4958

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17723470; hg19: chr11-45227567; COSMIC: COSV55443399; COSMIC: COSV55443399;